There was nothing in the ark except the two tablets that Moses had placed in it at Horeb, where the Lord made a covenant with the Israelites after they came out of Egypt. 2 Chronicles 5:10

            The ark was supposed to contain a number of items. 

This ark contained the gold jar of manna, Aaron’s staff that had budded, and the stone tablets of the covenant.  Hebrews 9:4

            But by the time it arrived in in the temple during Solomon’s reign Aaron’s staff and the jar of manna were missing.

            Since the time of Exodus to the time of the ark’s arrival in Solomon’s temple, nearly a thousand years had passed.  The ark sat in the desert, in people’s houses, in a tent during all that time.  It was carried into wars and transferred over enemy lines into Philistine territory.  Who knows who opened it and desecrated it.  Basically it was neglected and not shown the reference it deserved.

            Maybe the staff rotted and the manna was eaten by rodents.  It’s hard to say.  The sturdier stone tablets survived which showed that God’s law remained intact.